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Add scanpy #25

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merged 9 commits into from
Aug 26, 2024
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Merged

Add scanpy #25

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ee0f1d3
added Dockerfile for scanpy
Sanaz01 Apr 30, 2024
c5b82d6
install packages using single run
Sanaz01 Apr 30, 2024
38d67d8
add Dockerfile for scvi-tools
Sanaz01 Apr 30, 2024
5a32e9d
Install necessary packages only
Sanaz01 May 9, 2024
9b416ca
renamed Dockerfiles
Sanaz01 Aug 24, 2024
dc5f98f
Merge branch 'main' into add_scanpy
tefirman Aug 24, 2024
9fd7159
Adding no-cache-dir argument to pip
tefirman Aug 24, 2024
cbaf540
added no cache dir
Sanaz01 Aug 25, 2024
49fd599
Splitting pip into two calls because of index-url
tefirman Aug 26, 2024
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15 changes: 15 additions & 0 deletions scanpy/Dockerfile_latest
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# Using Python base image
FROM python:3.10-slim

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="scanpy"
LABEL org.opencontainers.image.description="Container image for the use of Scanpy library for Single-Cell analysis in Python"
LABEL org.opencontainers.image.version="latest"
LABEL org.opencontainers.image.authors="wilds@fredhutch.org"
LABEL org.opencontainers.image.url=https://hutchdatascience.org/
LABEL org.opencontainers.image.documentation=https://getwilds.org/
LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
LABEL org.opencontainers.image.licenses=MIT

# Installing packages via pip
RUN pip install --no-cache-dir scanpy==1.10.2 leiden-clustering==0.1.0
18 changes: 18 additions & 0 deletions scvi-tools/Dockerfile_latest
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# Using Python base image
FROM python:3.10-slim

# Adding labels for the GitHub Container Registry
LABEL org.opencontainers.image.title="scvi-tools"
LABEL org.opencontainers.image.description="Container image for the use of scvi-tools library for Single-Cell analysis in Python"
LABEL org.opencontainers.image.version="latest"
LABEL org.opencontainers.image.authors="wilds@fredhutch.org"
LABEL org.opencontainers.image.url=https://hutchdatascience.org/
LABEL org.opencontainers.image.documentation=https://getwilds.org/
LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
LABEL org.opencontainers.image.licenses=MIT

# Installing packages via pip
# For GPU enabled abilities (from https://pytorch.org/get-started/locally/) - torch, torchvision, torchaudio
RUN pip install --no-cache-dir scvi-tools==1.1.6 scanpy==1.10.2 leiden-clustering==0.1.0 scikit-misc==0.5.1 \
&& pip install --no-cache-dir torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu118